I think we would need a flag like "set picking dragSelected". We have set
pickingStyle select drag, but it really doesn't do much, and it it doesn't
allow for rotation, which I think is a nice feature of set picking
dragMolecule (with SHIFT).
OK, I have added for Jmol 12.1.46
set picking dragSelected
that acts like set picking dragMolecule, except it is the specific atoms
that have been selected, and pretty much deprecates
set pickingStyle select drag
see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Bob
On Mon, May 9, 2011 at 3:09 PM, Paul Pillot <paul.pil...@ac-orleans-tours.fr
> wrote:
> Yes ! I'm finally on Jmol's cutting edge !
> Here is my report :
> - no more gliding spiders with Bob's last version !
> - when a chain contains gaps the different pieces are split by the dragging
> process (for example : 1qln, 2bg9)
>
Is that good or bad? desired or not? The request is "dragmolecule" and split
chains are not single molecules.
> - to make chains go back to where they came from, I had to store the
> coordinates for each chain in a variable. It doesn't work if I use the
> coordinates for the whole model. eg :
> - "tempset ={*}.xyz.all" then move the chains around, "rotate compare {*}
> @tempset -2", makes a rotation of the whole scene but not of the different
> chains relative to each others.
>
right
> -"tempset={*a}.xyz.all", then move the chain A around, "rotate compare {*a}
> @tempseta -2"; makes a cool motion of the chain A back to where it came
> from. There is a problem though with solvent molecules (PDB ID 1gzx for
> example), where the solvent molecules are not moved when the chain with the
> same ID is dragged, but are moved when the rotate compare command is issued.
> To prevent that, I had to change slightly the atoms set : "tempset={*a and
> not solvent}.xyz.all" ; "rotate compare {*a and not solvent} @tempseta -2}
> It works great, even if the scene has been rotated.
>
>
> So, to use this feature it is required to store for each chain the initial
> coordinates as soon as the set picking dragmolecule command is issued. There
> is a question regarding the solvent : should it be included with the rest of
> the chain in the dragging process ?
>
Finally, I think it's a great tool for exploring complex molecules : you can
> imagine students pulling chains apart in order to study some other chains
> (as for display or restrict commands, but in an interactive manner). It
> could be great also as a teaching tool to introduce proteins quaternary
> structure. (plus many other applications !)
>
>
That was the idea. There will be limitations.
> -Paul
>
> Le 9 mai 2011 à 06:16, Robert Hanson a écrit :
>
> You need to store them in a variable at some point before you start moving
> things. Really, Paul, you are among the first to experiment with this, so
> understand that it could be trickier than I make it out to be!
>
> On Sun, May 8, 2011 at 3:29 PM, Paul Pillot <
> paul.pil...@ac-orleans-tours.fr> wrote:
>
>> It works great now ! Thanks Bob !
>> You mentioned in one of your previous messages that one can use the ROTATE
>> COMPARE command to move the chains smoothly back to where they came from.
>> I've seen in the docs that the ROTATE COMPARE command requires the
>> coordinates from the previous position to be stored (eg : {2.1}.all.xyz).
>>
>
> I think that's {2.1}.xyz.all -- xyz coordinates (all of them, as an
> array, not just the average). The "smooth change" would require that you
> have the coordinates specifically of the atoms that have been moved. In my
> case, I was moving the first model in the second file. So I saved just those
> coordinates. Might be tricky to set this up with any atoms the user moves.
> You can always get them back, but not necessarily smoothly. For that we
> might need a new "morph" command.
>
> Bob
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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